Finding plausible ligand unbinding pathways in complex protein environments is a critical step in molecular modeling—but it can also be frustrating. Even with sophisticated tools, the system may return incomplete or biologically implausible results.
One frequent pain point? The sampling region—or sampling box—for ligand motions isn’t well defined. This often leads to search processes that go nowhere or yield uninformative results.
Why the Sampling Box Matters
The Ligand Path Finder extension in SAMSON uses a variation of the Rapidly-exploring Random Tree (RRT) method to search for pathways. A key part of making that algorithm useful is setting up a sampling region where conformations are explored.
If your box is too small, the ligand will not find a viable unbinding pathway. If it’s misaligned with the exit channels in the protein, the method may waste time exploring irrelevant directions. Getting it right is essential and surprisingly non-trivial.
Choosing the Right Box Dimensions
In the tutorial example featuring Thiodigalactosid (TDG) and the Lactose permease protein, the sampling box is defined around the active ligand atoms with extra room in the direction of expected unbinding—here, toward the periplasmic side.
Here’s how it looks when properly set:
Once defined, the green sampling box appears in the viewport, as shown below:
This visual check allows a quick confirmation: does the box include enough space for ligand displacement along likely exit trajectories?
Tips for Effective Box Setup
- Orient your system first: You can align your protein with respect to the Cartesian axes using SAMSON’s Move editors and context menu options (e.g.,
Move selection > Align with Z-axis). - Use biological insight: If your protein is membrane-bound or known to release the ligand in a specific direction, design the box accordingly.
- Overshoot slightly: It’s often better to make the box slightly too big than too small. The algorithm won’t explore sparse regions without a reason, but it will fail if it can’t reach legitimate exits.
- Visualize early: Always manipulate the system to visualize the sampling box before running the planner. It only takes a second and can spare you hours of debugging.
Conclusion
Many users overlook the importance of a well-defined sampling box, blaming the path-finding algorithm when the issue lies instead with an overlooked setup step. Pay close attention to how your ligand and protein are positioned and to how the box is configured—this often makes the difference between success and failure.
To see a complete step-by-step example, visit the Ligand Path Finder documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON and explore its capabilities at https://www.samson-connect.net.